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MCL coexpression mm9:263: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000010!3.09e-16!11;UBERON:0002410!2.00e-13!9;UBERON:0002240!6.37e-08!6;UBERON:0005174!6.37e-08!6;UBERON:0001137!6.37e-08!6;UBERON:0001948!2.77e-07!5;UBERON:0002315!2.77e-07!5;UBERON:0004121!5.98e-07!95;UBERON:0000924!5.98e-07!95;UBERON:0006601!5.98e-07!95
|ontology_enrichment_uberon=UBERON:0000010!3.09e-16!11;UBERON:0002410!2.00e-13!9;UBERON:0002240!6.37e-08!6;UBERON:0005174!6.37e-08!6;UBERON:0001137!6.37e-08!6;UBERON:0001948!2.77e-07!5;UBERON:0002315!2.77e-07!5;UBERON:0004121!5.98e-07!95;UBERON:0000924!5.98e-07!95;UBERON:0006601!5.98e-07!95
|tfbs_overrepresentation_for_novel_motifs=0.0583385,0.67589,0.183547,0.261569,0.663089,0.279466,0.401081,0.540444,1.15057,0.0451956,0.104348,0.121026,0.0862057,0.828885,0.726136,0,0.719985,0.633675,0.708933,0.17599,0.960368,0.537836,0.133942,0.0812711,0.74741,0.458764,0.273327,0.306197,0.118643,0.168435,0.288134,0.335912,0.0163666,0.565328,0.23664,0.105131,0.35459,0.379077,0.51446,0.238943,0.39333,0.0874315,0.466473,0.0965249,1.01703,0.530272,0.590335,0.326867,0.482168,0.534336,0.247239,0.166621,1.11126,0.451112,0.465864,0.138517,0.129176,0.739382,0.411486,0.42597,0.320373,0.513381,0.909778,0.672548,0.144946,0.268299,0.584509,0.907487,0.849558,0.768874,0.373674,0.357014,0.102346,0.494514,0.584774,0.105383,1.07464,0.572368,0.307225,0.62578,0.360662,0.749016,0.171576,0.320433,0.397678,0.226889,0.12317,0.0842698,1.12833,1.06309,0.64713,1.03749,0.34595,0.418991,0.764088,0.683274,0.331969,0.348163,0.204536,0.224173,0.0147312,0.335693,0.436484,0.247661,0.246912,0.294151,1.43933,0.0973104,0.15524,0.342885,0.204221,0.437975,0.349606,0.106977,0.653522,0.0782207,0.655924,0.562977,0.260696,0.345519,0.499163,1.19423,0.461462,0.196253,2.81737,0.310043,0.132139,0.340627,0.58316,0.223308,0.422342,0.917571,0.556974,0.448841,0.673182,0.525812,0.22165,0.0880894,0.628575,1.42304,1.03234,0.588705,0.158669,0.344113,0.242322,0.295293,0.206447,1.38398,0.486947,0.0836696,0.465328,0.211987,0.452434,0.461241,0.447481,0.522448,0.167242,0.255755,0.209338,0.0614775,0.637161,0.396979,0.835186,0.201723,0.239991,0.141571,0.587533,0.766115,0.475095
|tfbs_overrepresentation_for_novel_motifs=0.0583385,0.67589,0.183547,0.261569,0.663089,0.279466,0.401081,0.540444,1.15057,0.0451956,0.104348,0.121026,0.0862057,0.828885,0.726136,0,0.719985,0.633675,0.708933,0.17599,0.960368,0.537836,0.133942,0.0812711,0.74741,0.458764,0.273327,0.306197,0.118643,0.168435,0.288134,0.335912,0.0163666,0.565328,0.23664,0.105131,0.35459,0.379077,0.51446,0.238943,0.39333,0.0874315,0.466473,0.0965249,1.01703,0.530272,0.590335,0.326867,0.482168,0.534336,0.247239,0.166621,1.11126,0.451112,0.465864,0.138517,0.129176,0.739382,0.411486,0.42597,0.320373,0.513381,0.909778,0.672548,0.144946,0.268299,0.584509,0.907487,0.849558,0.768874,0.373674,0.357014,0.102346,0.494514,0.584774,0.105383,1.07464,0.572368,0.307225,0.62578,0.360662,0.749016,0.171576,0.320433,0.397678,0.226889,0.12317,0.0842698,1.12833,1.06309,0.64713,1.03749,0.34595,0.418991,0.764088,0.683274,0.331969,0.348163,0.204536,0.224173,0.0147312,0.335693,0.436484,0.247661,0.246912,0.294151,1.43933,0.0973104,0.15524,0.342885,0.204221,0.437975,0.349606,0.106977,0.653522,0.0782207,0.655924,0.562977,0.260696,0.345519,0.499163,1.19423,0.461462,0.196253,2.81737,0.310043,0.132139,0.340627,0.58316,0.223308,0.422342,0.917571,0.556974,0.448841,0.673182,0.525812,0.22165,0.0880894,0.628575,1.42304,1.03234,0.588705,0.158669,0.344113,0.242322,0.295293,0.206447,1.38398,0.486947,0.0836696,0.465328,0.211987,0.452434,0.461241,0.447481,0.522448,0.167242,0.255755,0.209338,0.0614775,0.637161,0.396979,0.835186,0.201723,0.239991,0.141571,0.587533,0.766115,0.475095
|tfbs_overrepresentation_jaspar=MA0003.1;0.328739,MA0004.1;0.075713,MA0006.1;0.228715,MA0007.1;0.0693451,MA0009.1;0.356735,MA0014.1;0.348616,MA0017.1;0.272987,MA0019.1;0.221321,MA0024.1;0.322453,MA0025.1;0.553002,MA0027.1;1.91746,MA0028.1;0.0230932,MA0029.1;0.305809,MA0030.1;0.31081,MA0031.1;0.284004,MA0038.1;0.89669,MA0040.1;0.366712,MA0041.1;0.0464556,MA0042.1;0.371303,MA0043.1;0.435645,MA0046.1;0.385571,MA0048.1;0.364526,MA0050.1;0.311127,MA0051.1;0.155655,MA0052.1;1.73218,MA0055.1;0.0656494,MA0056.1;0,MA0057.1;0.664918,MA0058.1;0.156036,MA0059.1;0.381997,MA0060.1;0.116099,MA0061.1;0.310047,MA0063.1;0,MA0066.1;0.143893,MA0067.1;0.652366,MA0068.1;1.19329,MA0069.1;0.975461,MA0070.1;0.365675,MA0071.1;0.310039,MA0072.1;0.358914,MA0073.1;4.23588,MA0074.1;0.391044,MA0076.1;0.0318933,MA0077.1;0.905433,MA0078.1;0.175945,MA0081.1;0.192641,MA0083.1;0.434982,MA0084.1;0.958921,MA0087.1;0.399335,MA0088.1;0.559807,MA0089.1;0,MA0090.1;0.481928,MA0091.1;0.584863,MA0092.1;1.76058,MA0093.1;0.106412,MA0095.1;0,MA0098.1;0,MA0100.1;0.117472,MA0101.1;0.177595,MA0103.1;0.122326,MA0105.1;0.355784,MA0106.1;1.02229,MA0107.1;0.0280799,MA0108.2;0.237143,MA0109.1;0,MA0111.1;0.238061,MA0113.1;0.490789,MA0114.1;0.787303,MA0115.1;0.437985,MA0116.1;1.43356,MA0117.1;0.411186,MA0119.1;0.400754,MA0122.1;0.427622,MA0124.1;0.604388,MA0125.1;0.538769,MA0130.1;0,MA0131.1;0.623192,MA0132.1;0,MA0133.1;0,MA0135.1;0.466327,MA0136.1;0.419326,MA0139.1;0.00479353,MA0140.1;0.117411,MA0141.1;1.33852,MA0142.1;0.27329,MA0143.1;0.515613,MA0144.1;0.311788,MA0145.1;0.0245594,MA0146.1;0.0233321,MA0147.1;0.341028,MA0148.1;0.996586,MA0149.1;6.1348,MA0062.2;0.117118,MA0035.2;0.119926,MA0039.2;0.275067,MA0138.2;0.61046,MA0002.2;0.336369,MA0137.2;0.585976,MA0104.2;0.213989,MA0047.2;0.457516,MA0112.2;0.0575877,MA0065.2;0.197264,MA0150.1;0.0692983,MA0151.1;0,MA0152.1;0.457674,MA0153.1;0.480495,MA0154.1;0.221011,MA0155.1;0.0344296,MA0156.1;0.128979,MA0157.1;0.250083,MA0158.1;0,MA0159.1;0.365833,MA0160.1;0.0842824,MA0161.1;0,MA0162.1;0.609369,MA0163.1;0.533899,MA0164.1;0.419846,MA0080.2;0.523079,MA0018.2;0.433858,MA0099.2;1.77332,MA0079.2;0.411928,MA0102.2;1.0092,MA0258.1;0.273872,MA0259.1;0.533842,MA0442.1;0
}}
}}

Revision as of 11:27, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:67400252..67400263,+p9@Gas7
Mm9::chr11:95430349..95430358,-p@chr11:95430349..95430358
-
Mm9::chr11:95431175..95431200,-p@chr11:95431175..95431200
-
Mm9::chr11:95431260..95431274,-p@chr11:95431260..95431274
-
Mm9::chr11:95435706..95435720,-p@chr11:95435706..95435720
-
Mm9::chr11:95442317..95442326,-p@chr11:95442317..95442326
-
Mm9::chr11:95449005..95449021,-p1@Ngfr
Mm9::chr12:86692075..86692107,-p7@Tmed10
Mm9::chr13:63424826..63424833,-p@chr13:63424826..63424833
-
Mm9::chr14:105988723..105988748,+p2@uc007uxu.2
p2@uc011zpn.1
p2@uc011zpo.1
p2@uc011zpp.1
p2@uc011zpq.1
Mm9::chr14:105988749..105988763,+p1@uc007uxu.2
p1@uc011zpn.1
p1@uc011zpo.1
p1@uc011zpp.1
p1@uc011zpq.1
Mm9::chr14:105988833..105988840,+p1@ENSMUST00000134007
Mm9::chr15:7760041..7760056,+p@chr15:7760041..7760056
+
Mm9::chr15:98725842..98725863,-p@chr15:98725842..98725863
-
Mm9::chr17:14683348..14683368,+p@chr17:14683348..14683368
+
Mm9::chr17:14732894..14732899,+p@chr17:14732894..14732899
+
Mm9::chr19:58530274..58530285,-p12@Gfra1
Mm9::chr19:58530308..58530362,-p3@Gfra1
Mm9::chr19:58530393..58530404,-p14@Gfra1
Mm9::chr19:58530437..58530452,-p5@Gfra1
Mm9::chr3:57305697..57305724,-p@chr3:57305697..57305724
-
Mm9::chr4:129732267..129732291,+p6@Col16a1
Mm9::chr4:99323019..99323031,+p4@Foxd3
Mm9::chr6:31073236..31073239,+p@chr6:31073236..31073239
+
Mm9::chr6:83087097..83087115,+p9@Rtkn
Mm9::chr6:83087128..83087146,+p13@Rtkn
Mm9::chr7:137818145..137818172,+p@chr7:137818145..137818172
+
Mm9::chr8:11797411..11797448,+p@chr8:11797411..11797448
+
Mm9::chr8:49928618..49928674,-p@chr8:49928618..49928674
-
Mm9::chr8:49928714..49928733,-p@chr8:49928714..49928733
-
Mm9::chr8:49929234..49929248,-p@chr8:49929234..49929248
-
Mm9::chrX:149092305..149092326,-p@chrX:149092305..149092326
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0043121neurotrophin binding0.0220018627075001
GO:0017049GTP-Rho binding0.0220018627075001
GO:0001829trophectodermal cell differentiation0.0220018627075001
GO:0048199vesicle targeting, to, from or within Golgi0.0220018627075001
GO:0048406nerve growth factor binding0.0220018627075001
GO:0009653anatomical structure morphogenesis0.0274970545431882
GO:0042488positive regulation of odontogenesis of dentine-containing teeth0.0274970545431882
GO:0042482positive regulation of odontogenesis0.0274970545431882
GO:0042481regulation of odontogenesis0.0305347110597331
GO:0005095GTPase inhibitor activity0.0305347110597331
GO:0042589zymogen granule membrane0.0305347110597331
GO:0007399nervous system development0.0305347110597331
GO:0048667neuron morphogenesis during differentiation0.0305347110597331
GO:0048812neurite morphogenesis0.0305347110597331
GO:0005035death receptor activity0.0305347110597331
GO:0001825blastocyst formation0.0305347110597331
GO:0042588zymogen granule0.0305347110597331
GO:0042487regulation of odontogenesis of dentine-containing teeth0.0305347110597331
GO:0006903vesicle targeting0.0328181267948919
GO:0016048detection of temperature stimulus0.0328181267948919
GO:0000904cellular morphogenesis during differentiation0.0328181267948919
GO:0031175neurite development0.0328181267948919
GO:0005801cis-Golgi network0.0328181267948919
GO:0032502developmental process0.0328181267948919
GO:0048731system development0.0328181267948919
GO:0030667secretory granule membrane0.0328181267948919
GO:0048869cellular developmental process0.0328181267948919
GO:0030154cell differentiation0.0328181267948919
GO:0048666neuron development0.0328181267948919
GO:0021675nerve development0.0355230660621697
GO:0043588skin development0.0355230660621697
GO:0035257nuclear hormone receptor binding0.0355230660621697
GO:0051650establishment of vesicle localization0.0355230660621697
GO:0001892embryonic placenta development0.0355230660621697
GO:0051427hormone receptor binding0.0356708540809494
GO:0051648vesicle localization0.0356708540809494
GO:0032990cell part morphogenesis0.0356708540809494
GO:0048858cell projection morphogenesis0.0356708540809494
GO:0030030cell projection organization and biogenesis0.0356708540809494
GO:0051017actin filament bundle formation0.0356708540809494
GO:0048856anatomical structure development0.0358024264734813
GO:0030182neuron differentiation0.0361493430947323
GO:0017048Rho GTPase binding0.042373404854525
GO:0030041actin filament polymerization0.042373404854525
GO:0048699generation of neurons0.0432869659028584
GO:0007275multicellular organismal development0.0474875106611709
GO:0022008neurogenesis0.0474875106611709
GO:0051656establishment of organelle localization0.0479448740767939



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
autonomic neuron2.00e-139
ectodermal cell2.50e-1044
neurectodermal cell2.50e-1044
neural cell1.76e-0943
neuron2.47e-0833
neuronal stem cell2.47e-0833
neuroblast2.47e-0833
electrically signaling cell2.47e-0833
non-terminally differentiated cell1.48e-0749

Uber Anatomy
Ontology termp-valuen
peripheral nervous system3.09e-1611
autonomic nervous system2.00e-139
spinal cord6.37e-086
dorsal region element6.37e-086
dorsum6.37e-086
regional part of spinal cord2.77e-075
gray matter of spinal cord2.77e-075
ectoderm-derived structure5.98e-0795
ectoderm5.98e-0795
presumptive ectoderm5.98e-0795


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)
MA0003.10.328739
MA0004.10.075713
MA0006.10.228715
MA0007.10.0693451
MA0009.10.356735
MA0014.10.348616
MA0017.10.272987
MA0019.10.221321
MA0024.10.322453
MA0025.10.553002
MA0027.11.91746
MA0028.10.0230932
MA0029.10.305809
MA0030.10.31081
MA0031.10.284004
MA0038.10.89669
MA0040.10.366712
MA0041.10.0464556
MA0042.10.371303
MA0043.10.435645
MA0046.10.385571
MA0048.10.364526
MA0050.10.311127
MA0051.10.155655
MA0052.11.73218
MA0055.10.0656494
MA0056.10
MA0057.10.664918
MA0058.10.156036
MA0059.10.381997
MA0060.10.116099
MA0061.10.310047
MA0063.10
MA0066.10.143893
MA0067.10.652366
MA0068.11.19329
MA0069.10.975461
MA0070.10.365675
MA0071.10.310039
MA0072.10.358914
MA0073.14.23588
MA0074.10.391044
MA0076.10.0318933
MA0077.10.905433
MA0078.10.175945
MA0081.10.192641
MA0083.10.434982
MA0084.10.958921
MA0087.10.399335
MA0088.10.559807
MA0089.10
MA0090.10.481928
MA0091.10.584863
MA0092.11.76058
MA0093.10.106412
MA0095.10
MA0098.10
MA0100.10.117472
MA0101.10.177595
MA0103.10.122326
MA0105.10.355784
MA0106.11.02229
MA0107.10.0280799
MA0108.20.237143
MA0109.10
MA0111.10.238061
MA0113.10.490789
MA0114.10.787303
MA0115.10.437985
MA0116.11.43356
MA0117.10.411186
MA0119.10.400754
MA0122.10.427622
MA0124.10.604388
MA0125.10.538769
MA0130.10
MA0131.10.623192
MA0132.10
MA0133.10
MA0135.10.466327
MA0136.10.419326
MA0139.10.00479353
MA0140.10.117411
MA0141.11.33852
MA0142.10.27329
MA0143.10.515613
MA0144.10.311788
MA0145.10.0245594
MA0146.10.0233321
MA0147.10.341028
MA0148.10.996586
MA0149.16.1348
MA0062.20.117118
MA0035.20.119926
MA0039.20.275067
MA0138.20.61046
MA0002.20.336369
MA0137.20.585976
MA0104.20.213989
MA0047.20.457516
MA0112.20.0575877
MA0065.20.197264
MA0150.10.0692983
MA0151.10
MA0152.10.457674
MA0153.10.480495
MA0154.10.221011
MA0155.10.0344296
MA0156.10.128979
MA0157.10.250083
MA0158.10
MA0159.10.365833
MA0160.10.0842824
MA0161.10
MA0162.10.609369
MA0163.10.533899
MA0164.10.419846
MA0080.20.523079
MA0018.20.433858
MA0099.21.77332
MA0079.20.411928
MA0102.21.0092
MA0258.10.273872
MA0259.10.533842
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:263&oldid=2573658"